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-rwxr-xr-xwqflask/base/data_set.py2
-rwxr-xr-xwqflask/base/mrna_assay_tissue_data.py5
-rwxr-xr-xwqflask/wqflask/correlation/show_corr_results.py41
-rwxr-xr-xwqflask/wqflask/templates/show_trait_calculate_correlations.html10
4 files changed, 22 insertions, 36 deletions
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 427fd991..d6a46c2e 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -1257,7 +1257,7 @@ class MrnaAssayDataSet(DataSet):
Strain.Name
""" % (escape(trait), escape(self.name))
results = g.db.execute(query).fetchall()
- print("RETRIEVED RESULTS HERE:", results)
+ #print("RETRIEVED RESULTS HERE:", results)
return results
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index b2c0448a..54a7ce8e 100755
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -40,7 +40,6 @@ class MrnaAssayTissueData(object):
# with highest mean value
# Due to the limit size of TissueProbeSetFreezeId table in DB,
# performance of inner join is acceptable.MrnaAssayTissueData(gene_symbols=symbol_list)
- #print("len(gene_symbols): ", len(gene_symbols))
if len(gene_symbols) == 0:
query += '''Symbol!='' and Symbol Is Not Null group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
@@ -49,9 +48,11 @@ class MrnaAssayTissueData(object):
else:
in_clause = db_tools.create_in_clause(gene_symbols)
+ #ZS: This was in the query, not sure why: http://docs.python.org/2/library/string.html?highlight=lower#string.lower
+
query += ''' Symbol in {} group by Symbol)
as x inner join TissueProbeSetXRef as t on t.Symbol = x.Symbol
- and t.Mean = x.maxmean;http://docs.python.org/2/library/string.html?highlight=lower#string.lower
+ and t.Mean = x.maxmean;
'''.format(in_clause)
results = g.db.execute(query).fetchall()
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index af8bb2ab..2612857f 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -112,19 +112,19 @@ class CorrelationResults(object):
self.p_range_lower = float(start_vars['p_range_lower'])
self.p_range_upper = float(start_vars['p_range_upper'])
- if ('min_loc_chr' in start_vars and
- 'max_loc_chr' in start_vars and
+ if ('loc_chr' in start_vars and
'min_loc_mb' in start_vars and
'max_loc_mb' in start_vars):
- self.min_location_chr = start_vars['min_loc_chr']
- self.max_location_chr = start_vars['max_loc_chr']
+ self.location_chr = start_vars['loc_chr']
if start_vars['min_loc_mb'].isdigit():
self.min_location_mb = start_vars['min_loc_mb']
else:
- self.min_location_mb = 0
+ self.min_location_mb = None
if start_vars['max_loc_mb'].isdigit():
self.max_location_mb = start_vars['max_loc_mb']
+ else:
+ self.max_location_mb = None
self.get_formatted_corr_type()
self.return_number = int(start_vars['corr_return_results'])
@@ -149,7 +149,6 @@ class CorrelationResults(object):
if corr_samples_group == 'samples_other':
primary_samples = [x for x in primary_samples if x not in (
self.dataset.group.parlist + self.dataset.group.f1list)]
- print("primary_samples:", primary_samples)
self.process_samples(start_vars, self.this_trait.data.keys(), primary_samples)
self.target_dataset = data_set.create_dataset(start_vars['corr_dataset'])
@@ -185,16 +184,12 @@ class CorrelationResults(object):
if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno":
#ZS: Convert min/max chromosome to an int for the location range option
- min_chr_as_int = 1
- max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing
+ range_chr_as_int = None
for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
- if chr_info.name == self.min_location_chr:
- min_chr_as_int = order_id
- if chr_info.name == self.max_location_chr:
- max_chr_as_int = order_id
+ if chr_info.name == self.location_chr:
+ range_chr_as_int = order_id
for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
- print("trait name:", trait)
trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True)
if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno":
@@ -207,15 +202,15 @@ class CorrelationResults(object):
if (float(self.correlation_data[trait][0]) >= self.p_range_lower and
float(self.correlation_data[trait][0]) <= self.p_range_upper):
- if ((self.dataset.type == "ProbeSet" or self.dataset.type == "Geno") and
- (self.min_expr != None and float(trait_object.mean) >= self.min_expr) and
- chr_as_int >= min_chr_as_int and
- chr_as_int <= max_chr_as_int) :
-
+ if self.dataset.type == "ProbeSet" or self.dataset.type == "Geno":
- if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)):
+ if (self.min_expr != None) and (float(trait_object.mean) < self.min_expr):
+ continue
+ elif range_chr_as_int != None and (chr_as_int != range_chr_as_int):
+ continue
+ elif (self.min_location_mb != None) and (float(trait_object.mb) < float(self.min_location_mb)):
continue
- elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)):
+ elif (self.max_location_mb != None) and (float(trait_object.mb) > float(self.max_location_mb)):
continue
(trait_object.sample_r,
@@ -501,8 +496,6 @@ class CorrelationResults(object):
FROM GeneIDXRef
WHERE rat='%s'""" % escape(gene_id)
- print("GENE_ID QUERY: ", query)
-
result = g.db.execute(query).fetchone()
if result != None:
mouse_gene_id = result.mouse
@@ -513,13 +506,9 @@ class CorrelationResults(object):
FROM GeneIDXRef
WHERE human='%s'""" % escape(gene_id)
- print("GENE_ID QUERY: ", query)
-
result = g.db.execute(query).fetchone()
if result != None:
mouse_gene_id = result.mouse
-
- print("mouse_geneid:", mouse_gene_id)
return mouse_gene_id
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index 3203c0c4..68cc8b18 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -82,15 +82,11 @@
<div class="form-group">
<label class="col-xs-1 control-label">Location</label>
<div class="col-xs-4 controls">
- <span style="margin:10px;">
- Min Chr: <input name="min_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">
- Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+ <span>
+ Chr: <input name="loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">&nbsp;&nbsp;&nbsp;
+ Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;"> &nbsp;to&nbsp; <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
</span>
<br>
- <span style="margin:10px;">
- Max Chr: <input name="max_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">
- Mb: <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
- </span>
</div>
</div>
{% endif %}